ggplot2 is not printing all the information I need in R - json

Question

I am trying to replicate the following script: San Francisco Crime Classification
here is my code:
library(dplyr)
library(ggmap)
library(ggplot2)
library(readr)
library(rjson)
library(RCurl)
library(RJSONIO)
library(jsonlite)
train=jsonlite::fromJSON("/home/felipe/Templates/Archivo de prueba/databritanica.json")
counts <- summarise(group_by(train, Crime_type), Counts=length(Crime_type))
#counts <- counts[order(-counts$Crime_type),]
# This removes the "Other Offenses" category
top12 <- train[train$Crime_type %in% counts$Crime_type[c(1,3:13)],]
map<-get_map(location=c(lon = -2.747770, lat = 53.389499) ,zoom=12,source="osm")
p <- ggmap(map) +
geom_point(data=top12, aes(x=Longitude, y=Latitude, color=factor(Crime_type)), alpha=0.05) +
guides(colour = guide_legend(override.aes = list(alpha=1.0, size=6.0),
title="Type of Crime")) +
scale_colour_brewer(type="qual",palette="Paired") +
ggtitle("Top Crimes in Britain") +
theme_light(base_size=20) +
theme(axis.line=element_blank(),
axis.text.x=element_blank(),
axis.text.y=element_blank(),
axis.ticks=element_blank(),
axis.title.x=element_blank(),
axis.title.y=element_blank())
ggsave("united kingdom_top_crimes_map.png", p, width=14, height=10, units="in")
I am reading the data from a JSON file and try to print points over the map according to the data. Each point is a type of crime that is have been committed, the location of each point depends of two parameters: longitude and latitude.
What is the problem? the points are not being printing. The script generate a new map without the points that is suppose to show.
This is the original map:
And this is the result:
Any ideas??
This a example of the data contain in the JSON file is:
[
{"Month":"2014-05","Longitude":-2.747770,"Latitude":53.389499,"Location":"On or near Cronton Road","LSOA_name":"Halton 001B","Crime_type":"Other theft"},
{"Month":"2014-05","Longitude":-2.799099,"Latitude":53.354676,"Location":"On or near Old Higher Road","LSOA_name":"Halton 008B","Crime_type":"Anti-social behaviour"},
{"Month":"2014-05","Longitude":-2.804451,"Latitude":53.352456,"Location":"On or near Higher Road","LSOA_name":"Halton 008B","Crime_type":"Anti-social behaviour"}
]

Answer 1

Short answer:
Your alpha = 0.05 is making the points practically invisible when plotted on the colorful map background, as mentioned by #aosmith.
Longer answer:
I suggest the following changes to your geom_point:
Increase the alpha to something more reasonable
Increase the size of the points
Optionally, change the shape to one with a background and fill for better visibility
This will require you to change the fill parameter in aes, as well as the scale_color_brewer to scale_fill_brewer
Example:
# Load required packages
library(dplyr)
library(ggplot2)
library(ggmap)
library(jsonlite)
# Example data provided in question, with one manually entered entry with
# Crime_type = "Other Offenses"
'[
{"Month":"2014-05","Longitude":-2.747770,"Latitude":53.389499,"Location":"On or near Cronton Road","LSOA_name":"Halton 001B","Crime_type":"Other theft"},
{"Month":"2014-05","Longitude":-2.799099,"Latitude":53.354676,"Location":"On or near Old Higher Road","LSOA_name":"Halton 008B","Crime_type":"Anti-social behaviour"},
{"Month":"2014-05","Longitude":-2.804451,"Latitude":53.352456,"Location":"On or near Higher Road","LSOA_name":"Halton 008B","Crime_type":"Anti-social behaviour"},
{"Month":"2014-05","Longitude":-2.81,"Latitude":53.36,"Location":"On or near Higher Road","LSOA_name":"Halton 008B","Crime_type":"Other Offenses"}
]' -> example_json
train <- fromJSON(example_json)
# Process the data, the dplyr way
counts <- train %>%
group_by(Crime_type) %>%
summarise(Counts = length(Crime_type))
# This removes the "Other Offenses" category
top12 <- train %>%
filter(Crime_type != "Other Offenses")
# Get the map
map <- get_map(location=c(lon = -2.747770, lat = 53.389499), zoom=12, source="osm")
# Plotting code
p <- ggmap(map) +
# Changes made to geom_point.
# I increased the alpha and size, and I used a shape that has
# a black border and a fill determined by Crime_type.
geom_point(data=top12, aes(x=Longitude, y=Latitude, fill=factor(Crime_type)),
shape = 21, alpha = 0.75, size = 3.5, color = "black") +
guides(fill = guide_legend(override.aes = list(alpha=1.0, size=6.0),
title="Type of Crime")) +
# Changed scale_color_brewer to scale_fill_brewer
scale_fill_brewer(type="qual", palette="Paired") +
ggtitle("Top Crimes in Britain") +
theme_light(base_size=20) +
theme(axis.line=element_blank(),
axis.text.x=element_blank(),
axis.text.y=element_blank(),
axis.ticks=element_blank(),
axis.title.x=element_blank(),
axis.title.y=element_blank())